Hello Christian,
I found this FAQ on the IGV web site. They may be the best resource for resolving display issues if they continue. Comparing results between IGV and Galaxy's visualization tool Trackster can help you to determine the root cause of the problem. http://www.broadinstitute.org/software/igv/BAM http://www.broadinstitute.org/igv/FAQ
Hopefully this helps point you in the right direction,
Best,
Jen Galaxy team
On 7/31/11 6:04 PM, Cristian Rojas wrote:
Hi people, I have a litle problem with Bowtie alignments. I am tryin to align sRNA Illumina dataset to hairpin mirbase. The problem is that after the steps (detailed below) I only obtain reads of 15-18nt, and I know that I have a lot of microRNAs (20-22nt) in my data. Beside the size problem, I realized that when the reads and the reference (the precursor in any case) the sequences don't match as I would expect. The sequential steps that I've made:
- Groom
- Clip (adaptor elimination)
- Bowtie against hairpin database (mirBase precursor)
- SAM-to-BAM
- Download Bam and Bai files
- Open in IGV the file and the hairpin database
May be I am doing something really bad, but I dont know. Any help/suggestion/tip? Thanks in advance
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